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Department of Chemical Engineering, University of Bath

Surface area program

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Calculating the accessible surface area
File containing the atom diameters

The diameters of the framework atoms are defined in this file. These would normally be the Lennard Jones sigma from a force field. There are two points to note:

• The values for the accessible surface area will vary slightly depending on the choice of force field


• Quite often, in the force field papers not the Lennard Jones sigma parameter is given but the value for the minimum of the potential. So you might have to convert the tabulated values. For example, the values tabulated in the UFF force field (which has been used in the examples here), D0, are given as the values at the minimum of the potential. To convert use: sigma = D0 / 2^(1/6)

For the sample file , the diameters were taken from the UFF force field ( A.K. Rappe et al., J. Am. Chem. Soc. 1992 114, 10024.). Make sure that your diameter file contains all the atoms present in your framework and that the names are the same in the coordinate file and the diameter file. Otherwise the program will stop with an error message.


C 3.431
O 3.118
Zn 2.462
H 2.571
Cd 2.537
Cr 2.693
EOF


The file contains a list of the atom names (make sure they are the same as in your coordinate file or the program will stop with an error message!) and the diameters in Angstrom. "EOF" denotes the end of the file. Make sure that all framework atom types are listed or the program will stop with an error message!